Personal

My husband, Mehmet Berkmen, is also a microbiologist. He was a post-doc in Jon Beckwith's lab at Harvard Medical School.http://beck2.med.harvard.edu/
Now he is at the biotech company New England Biolabs, where he is developing Escherichia coli strains and plasmids for recombinant protein production.http://www.neb.com/nebecomm/default.asp.

Here are some of the things that I am doing when I am not in the scope room, cooking, or learning Turkish:

Teaching and supervisory experience

(Fall 2005) Co-instructor for an undergraduate seminar class at MIT
I co-taught a literature-based class on DNA dynamics in the tiny bacterial cell with Lyle Simmons. Each week we discussed two papers exploring bacterial DNA replication, chromosome and plasmid partitioning, conjugation, or cell shape.
http://web.mit.edu/biology/www/undergrad/adv-ugsem.html

(2005-present) Question consultant for the 2005 National Biology Olympiad
for high school students in collaboration with the Center for Excellence in Education in McLean, VA
http://www.cee.org/usabo/index.shtml

(Each Spring 2004-present) Volunteer assistant/instructor for the "Science Field Trip to MIT"
that involved ~90 students from four Boston area high schools and their teachers. In 2004, I helped run a lab exercise based on microscopic observation of zebrafish embryos. In 2005 and 2006, Jenny Auchtung and I designed and ran a lab exercise based on bacterial responses to starvation and stress. We had the high school students act as CSI agents and discover whether the "mysterious white powder" found in an envelope was Bacillus spores or harmless.
http://www.cfkeep.org/html/snapshot.php?id=84010578

Research

1. How do proteins come together to form a functional molecular machine, capable of complex tasks such as RNA synthesis or DNA transport?

2. How are the proteins that make up a complex molecular machine targeted to the correct location in the cell in order for them to function properly.

My interest in understanding how molecular machines function began with my graduate work on Escherichia coli RNA polymerase (RNAP). Employing biochemical, biophysical, and molecular genetic methods, I investigated the mechanistic details by which the small molecule guanosine tetraphosphate (ppGpp) acts as both a positive and negative regulator of transcription initiation in E. coli. I found that ppGpp shortens the half-lives of RNAP-promoter complexes formed on all promoters, even those promoters unaffected by ppGpp in vivo. The kinetic properties of a particular promoter determined whether or not the effect of ppGpp on half-life results in inhibition. Furthermore, I found that ppGpp stimulated amino acid promoter activity in vivo, but not in purified transcription assays. These and other data led me to propose that direct inhibition of the highly transcribed rRNA genes by ppGpp results in a dramatic increase in the free RNAP concentration, which leads to an increase in initiation from amino acid biosynthesis promoters that are rate-limited for binding RNAP. My results demonstrated that dissecting the details of the interactions between molecules (in this case, RNAP, promoter DNA, and ppGpp) could provide keys to understanding complex physiological phenomena.

For my postdoctoral work, I turned to the broad question of how molecular machines are localized to their correct subcellular addresses in bacteria. My work initially focused on how the replication machinery and the origin of replication are positioned in B. subtilis and whether the location of one influences the position of the other. I found that the replication machinery co-localizes with the origin immediately after initiation, indicating that replication initiates near midcell. Several lines of evidence indicated that the location of the origin at the time of initiation establishes the position of the replication machinery. I also discovered that origin positioning is independent of origin sequences and the site of replication initiation. My results provide new insights into how the replication machinery is dynamically positioned in the cell and refine our current understanding of the spatial and temporal events of the B. subtilis replication cycle.

My current research focus also uses B. subtilis as a model system but has shifted to exploring the function and subcellular localization of a different complex molecular machine, the Gram-positive mating pore. I have been characterizing YddE, a protein that is essential for mating of the B. subtilis conjugal element ICEBs1. yddE is encoded on ICEBs1 and is related to genes on conjugal elements in numerous bacteria, including the Gram-positive pathogens Staphylococcus aureus, Clostridium difficile, and L. monocytogenes. Containing Walker A and B box ATPase motifs, YddE belongs to a large superfamily of ATP-dependent pumps involved in the extrusion of proteins and DNA through membrane pores. Given the precedent of Gram-negative conjugation systems and given YddE’s localization, ATPase domain, and essentiality in conjugation, I propose that YddE and its homologs are the essential membrane-associated ATPase component of the Gram-positive mating pore apparatus. I plan on analyzing the role of YddE in conjugation, exploring its functional domains, investigating its subcellular localization, and identifying any YddE-interacting proteins.

Publications

Berkmen MB and Grossman AD. (2007) Subcellular positioning of the origin region of the Bacillus subtilis chromosome is independent of sequences within oriC, the site of replication initiation, and the replication initiator DnaA. Mol Microbiol, 63(1): 150-165.